1ID9

STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF RH(NH3)6+++

Summary for 1ID9

• Entry DOI: 10.2210/pdb1id9/pdb
• Related: 1ICG
• Descriptor: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3', RHODIUM HEXAMINE ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: rna/dna hybrid, fluoro uracil, rhodium(iii) hexammine, c-u mismatch, g-u mismatch, dna-rna complex, dna/rna
• Total number of polymer chains: 2
• Total formula weight: 6134.47

Authors

Cruse, W.,Saludjian, P.,Neuman, A.,Prange, T. (deposition date: 2001-04-04, release date: 2001-04-12, Last modification date: 2023-08-09)

Primary citation

Cruse, W.,Saludjian, P.,Neuman, A.,Prange, T.
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.
Acta Crystallogr.,Sect.D, 57:1609-1613, 2001

PubMed Abstract: In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.

PubMed: 11679725
DOI: 10.1107/S0907444901012318

Experimental method

X-RAY DIFFRACTION (1.6 Å)